Rna virus vaccines and methods

ABSTRACT

The invention is a vaccine, and method of vaccination, against RNA viruses, including RNA viruses in the family Flaviviridae, which includes for example West Nile Virus, Yellow fever virus, Dengue fever virus, Hepatitis C virus, Pestiviruses, Bovine viral diarrhea virus, and Classical Swine fever virus, wherein the vaccine comprises the RNA virus or immunogenic portions thereof, which have been treated with and rendered non-pathogenic by a phenothiazine dye and visible light. The invention includes novel strains of WNV for use in producing a vaccine.

CROSS-REFERENCE TO RELATED APPLICATIONS

The present application is a divisional of U.S. Ser. No. 11/639,023filed Dec. 14, 2006, now U.S. Pat. No. 7,767,210, which claims thebenefit under 35 U.S.C. 119(e) of U.S. Provisional Application Ser. No.60/750,859, filed Dec. 14, 2005. The entire disclosures of bothapplications are hereby expressly incorporated herein by reference.

STATEMENT REGARDING FEDERALLY SPONSORED RESEARCH OR DEVELOPMENT

Not Applicable.

BACKGROUND

The unstable nature of the RNA molecule enables RNA viruses to evolvefar more rapidly than DNA viruses, frequently changing their surfacestructures. RNA viruses in general have very high mutation rates as theylack polymerases which can find and fix mistakes, and are thereforeunable to conduct repair of damaged genetic material. DNA viruses haveconsiderably lower mutation rates due to the proofreading ability of DNApolymerases within the host cell. These mutations of RNA viruses make itmore difficult for an organism to develop any kind of lasting immunityto the virus. Because each surviving virus can reproduce itself hundredsor thousands of times, mutations in the RNA sequence occur frequently.It has been estimated that a typical RNA virus may experiencealterations of between 0.03 and 2 percent of its entire genome each yearthus evolving faster than any other living organism. Mutations occurrandomly across the entire length of the viral RNA, and so of coursemost are not beneficial, producing viruses which lack a needed proteinor are otherwise disadvantaged. However, because of the enormous numberof offspring produced by each virus, even a high rate of mutation doesnot threaten the survival of the virus, and when advantageous mutationsdo occur, they are rapidly selected for and reproduced. This evolutionis known as antigenic drift. Thus at least one reason for the lack ofsuitable vaccines against most RNA viruses is the high rate ofmutability of RNA viruses.

The West Nile Virus (WNV) of the Flaviviridae is such an RNA virus forwhich a vaccine is not available. WNV was first identified in 1937 inAfrica and first found in North America in 1999. Migratory birds areconsidered the primary means whereby infection is spread within andbetween countries. The virus is transmitted by mosquitoes that haveacquired infection by feeding on viremic birds. The virus is thenamplified during periods of adult mosquito blood-feeding. Infectedmosquitoes then transmit the virus to humans and animals upon feedingthereon.

WNV belongs to the Flaviviradae, a family of over 70 related viruses.WNV is an enveloped single-stranded positive sense RNA virus with agenome of approximately 11 kb encoding for three structural genes andseven non-structural genes.

West Nile Virus is the causative agent for West Nile Virus disease,particularly West Nile encephalitis, predominately in humans, othermammals and birds. The chief concern in both the United States andforeign countries is the lack of effective treatment for West Nile Virusdisease. Anti-inflammatory drugs are used to combat swelling of centralnervous system tissues, but beyond that no medical intervention iscurrently available.

The West Nile fever virus also affects horses, particularly in NorthAmerica and Europe. These horses reveal signs of ataxia, weakness of therear limbs, paresis evolving towards tetraplegia and death. Horses andcamels are the main animals manifesting clinical signs in the form ofencephalitis.

The virions of the West Nile fever virus are spherical particles with adiameter of 50 nm constituted by a lipoproteic envelope surrounding anicosahedric nucleocapsid containing a positive polarity, single-strandRNA. A single open reading frame (ORF) encodes all the viral proteins inthe form of a polyprotein. The cleaving and maturation of thispolyprotein leads to the production of several different viral proteins.The structural proteins are encoded by the 5′ part of the genome andcorrespond to the nucleocapsid designated C (14 kDa), the envelopglycoprotein designated E (50 kDa), the pre-membrane protein designatedprM (23 kDa), and the membrane protein designated M (7 kDa). Thenon-structural proteins are encoded by the 3′ part of the genome andcorrespond to the proteins NS1 (40 kDa), NS2A (19 kDa), NS2B (14 kDa),NS3 (74 kDa), NS4A (15 kDa), NS4B (29 kDa), and NS5 (97 kDa).

Recent reports show that WNV can also be passed from human to human byblood transfusion. With the recent epidemic increase in WNV prevalencein the U.S. (CDC, 1999, 2002; Enserink, 2002; Lanciotti et al, 1999), arise in WNV positive blood donors and rising need for methods toinactivate WNV in blood products can be expected.

Potential vaccines for WNV are described, for example, in U.S. PatentPublication Nos. 2003/0148261A1, 2003/0104008A1 and 2003/0091595A1.Publication No. 2003/0091595A1 describes a WNV vaccine that includes aninactivated whole or subunit WNV. Publication No. 2003/0104008A1discloses a vector, such as recombinant avipox virus, containing andexpressing exogenous polynucleotide(s) from WNV to induce an immuneresponse against WNV. These recombinant WNV vaccines include a vectorcontaining a polynucleotide having a single encoding frame correspondingto, for example, prM-E, M-E and prM-M-E. The vector may include severalseparate polynucleotides encoding the different proteins (e.g., prMand/or M and E). The vector can also include polynucleotidescorresponding to more than one WN virus strain, for example, two or morepolynucleotides encoding E or prM-M-E of different strains. Furthermore,the vector can include one or more nucleotide sequences encodingimmunogens of other pathogenic agents and/or cytokins. Publication No.2003/0148261A1 describes various WNV polypeptides and immunogenicfragments for use in WNV vaccines. These vaccines are producedrecombinantly using various vectors encoding WNV polypeptides and thevectors are expressed by a variety of host cells.

Methylene Blue (3,7-Bis(dimethylamino)phenothiazin-5-ium chloride), alsoreferred to herein as MB, is FDA approved for oral administration andhas been reported to be effective as an antiseptic, disinfectant, andantidote for cyanide and nitrate poisoning. The drug MB has seen limiteduse to inactivate HIV in blood products (Lambrecht et al, 1991; Mohr etal, 2004).

Further it is known that MB and other phenothiazine dyes (e.g., neutralred, thionine, and toluidene blue) can, in combination with wavelengthsof visible light (e.g., 660 nm) inactivate certain viruses (e.g., U.S.Pat. No. 6,348,309 and U.S. Pat. No. 6,346,529).

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 shows images of a plaque assay for OK02 and OK03 isolates of WNVon Vero cells at 4× magnification (A) or 40× magnification (B).

FIG. 2 shows how MB and light inactivates OK02 (A) and OK03 (B) invitro.

FIG. 3 shows that MB-inactivated virus does not cause disease in mice.

FIG. 4: Effects of active WNV (A and B) without prior immunization,after prior immunization of an immunocompetent mouse with MB-inactivatedWNV (C), and after prior immunization with MB-inactivated WNV of animmunodeficient mouse (D) on mouse survival (dosage 10⁴ pfu).

FIGS. 5 A and B shows Agarose gel images of amplification products from18 WNV specific primers.

FIG. 6: Anti-WNV specific IgG antibody titers after immunization eitherintra muscular (IM) or intra peritoneal (IP) of mice with MB-inactivatedWNV.

FIG. 7: Anti-WNV specific IgM antibody titers after intra muscular (IM)or intra peritoneal (IP) immunization of mice with MB-inactivated WNV.

FIG. 8: Effects of intra muscular (IM) or intra peritoneal (IP)immunization with MB-inactivated WNV on mouse survival after challengewith WNV (dosage 10³ pfu).

DESCRIPTION OF THE INVENTION

The present invention in one embodiment is directed to a vaccine againstRNA viruses, particularly those in the family Flaviviridae, whichincludes for example West Nile Virus, Yellow fever virus, Dengue fevervirus, Hepatitis C virus, Pestiviruses, Bovine viral diarrhea virus, andClassical Swine fever virus (and others as described elsewhere herein).The vaccine comprises at least one virus, or one or more immunogenicportions thereof, which have been treated with and renderednon-pathogenic by a phenothiazine dye and visible light. Moreparticularly, the RNA virus or immunogenic portion thereof may have beenrendered non-pathogenic by phenothiazine dyes, including, but notlimited to, Methylene Blue (MB), Methylene Green, 1-methyl MB,1,9-dimethyl MB, Azure A, Azure B, Azure C, thionine, and toluidineblue, or by squalene. More broadly, the invention comprises a vaccine orcomposition comprising an RNA virus or immunogenic portions thereofwhich have been rendered non-pathogenic by chemicals which induceRNA:RNA or RNA:protein crosslinking.

Further, the invention contemplates vaccines produced via the aboveinactivation techniques which are directed against any RNA virusincluding, but not limited to influenza, HIV and National Institute ofAllergy and Infectious Diseases (NIAID) Category A, B and C prioritypathogenic viruses and other RNA viruses described elsewhere herein.

Animal RNA viruses can be placed into about four different groupsdepending on their mode of replication, including:

-   -   (1) Positive-sense viruses which have their genome directly        utilized as if it were mRNA, producing a single protein which is        modified by host and viral proteins to form the various proteins        needed for replication. One of these includes RNA replicase,        which copies the viral RNA to form a double-stranded replicative        form which in turn directs the formation of new virions;    -   (2) Negative-sense viruses which must have their genome copied        by a RNA polymerase or transcriptase to form positive-sense RNA.        This positive-sense RNA molecule acts as viral mRNA, which is        translated into proteins by the host ribosomes. The resultant        protein goes on to direct the synthesis of new virions, such as        capsid proteins and RNA replicase, which is used to produce new        negative-sense RNA molecules;    -   (3) Double-stranded reoviruses which contain up to a dozen        different RNA molecules which each code for a mRNA. These all        associate with proteins to form a single large complex which is        replicated using virally-encoded replicase to form new virions;        and    -   (4) Retroviruses which are single-stranded but unlike other        single-stranded RNA viruses they use DNA intermediates to        replicate. Reverse transcriptase, a viral enzyme that comes form        the virus itself after it is uncoated, converts the viral RNA        into a complementary strand of DNA, which is copied to produce a        double stranded molecule of viral DNA which goes on to direct        the formation of new virions.

Because of the high rates of mutability of RNA viruses as noted above,it would be desirable to have a method such as that described herein forquickly manufacturing new or modified vaccines based on newly evolvingstrains of RNA viruses.

RNA viruses which could be treated and modified as described herein formanufacturing novel vaccines include, but are not limited to, those inthe following RNA virus families:

Arenaviridae, such as lymphcytic choriomeningitis virus (LCM), Lassavirus, Junin, Tacaribe, Pichinde viruses, Machupo virus, and Guanitovirus;

Bornaviridae, such as Borna disease virus;

Bunyaviradae, such as Hanta virus, California encephalitis virus,Japanese encephalitis virus, LaCrosse virus, Rift Valley fever virus,Bunyavirus, Arbovirus, Nairobi sheep disease virus, Phlebovirus, andTospoviruses;

Caliciviridae, such as Human and animal caliciviruses;

Coronaviridae, such as SARS Coronavirus;

Filoviridae, such as Ebola virus and Marburg virus;

Flaviviridae, such as Yellow Fever virus, Dengue Fever virus, West Nilevirus, Hepatitis C virus, Pestiviruses, Bovine Viral Diarrhea virus, andClassical Swine Fever virus (and others as indicated below);

Nodaviridae, such as Nodaviruses;

Orthomyxoviridae, such as Influenza virus type A, Influenza virus typeB, Influenza virus type C, Thogotovirus, and Fowl Plague disease virus;

Paramyxoviridae, such as Parainfluenza viruses, Mumps virus, Measlesvirus, Subacute sclerosing panencephalitis (SSPE) virus, Respiratorysyncytial virus (RSV), Pneumoviruses, “TPMV-like viruses”, NewcastleDisease virus, Rinderpest virus, and Canine Distemper virus;

Picornaviridae, such as Human Enteroviruses, including Poliovirus,

Coxsackie virus A, Coxsackie virus B, Hepatitis A virus, andRhinoviruses, Foot and Mouth Disease virus, Enterovirus 70,Apthoviruses, and Cardioviruses;

Reoviridae, such as Colorado Tick fever virus, Rotaviruses, Reoviruses,Coltivirus and Orbiviruses;

Retroviridae, such as Human immunodefficiency virus (HIV), HumanT-lymphotrophic virus (HTLV), Feline Leukemia virus (FeLV), FriendLeukemia virus (FLV), and MMTV (Mouse Mammary Tumor virus);

Rhabdoviridae, such as Rabies virus, and Vesicular Stomatitis virus; and

Togaviridae, such as Eastern Equine Encephalitis virus, Western EquineEncephalitis virus, Rubella virus (measles), Alphaviruses, and RossRiver virus.

More particularly, viruses in the Flaviviridae for which vaccines can beproduced using the methods of the present invention include, forexample, those in the genera Flavivirus and Pestivirus, the “HepatitisC-like viruses”, and those in the Yellow fever virus group, Tick-borneencephalitis virus group, Rio Bravo group, Japanese encephalitis group,Tyuleniy group, Ntaya group, Uganda S group, Dengue group, and Modocgroup. More specifically, the viruses of the Flaviviridae which may beused in the present invention include, for example, but are not limitedto, Gadgets Gully virus, Kyasanur Forest disease virus, Langat virus,including the British, Irish, Louping ill, Spanish and Turkish subtypes,Omsk hemorrhagic fever virus, Powassan virus, Karshi virus, Royal Farmvirus, Tick-borne encephalitis virus, including the European, FarEastern, and Siberian subtypes, Kadam virus, Meaban virus, Saumarez Reefvirus, Tyuleniy virus, Aroa virus, Bussuquara virus, Iguape virus,Naranjal virus, Dengue virus 1, Dengue virus 2, Dengue virus 3, Denguevirus 4, Kedougou virus, Cacipacore virus, Japanese encephalitis virus,Koutango virus, Alfuy virus, Murray Valley encephalitis virus, St. Louisencephalitis virus, Usutu virus, Kunjin virus, West Nile virus, Yaoundevirus, Kokobera virus, Stratford virus, Bagaza virus, Ilheus virus,Rocio virus, Israel turkey meningoencephalomyelitis virus, Ntaya virus,Tembusu virus, Spondweni virus, Zika virus, Banzi virus, Bouboui virus,Edge Hill virus, Jugra virus, Potiskum virus, Saboya virus, Sepik virus,Uganda S virus, Wesselsbron virus, Yellow fever virus, Entebbe batvirus, Sokoluk virus, Yokose virus, Apoi virus, Cowbone Ridge virus,Jutiapa virus, Modoc virus, Sal Vieja virus, San Perlita virus, Bukalasabat virus, Carey Island virus, Dakar bat virus, Montana myotisleukoencephalitis virus, Batu Cave virus, Phnom Penh bat virus, RioBravo virus, Cell fusing agent virus, Tamana bat virus, Border diseasevirus—BD31, Border disease virus—X818, Bovine viral diarrhea virus1-CP7, Bovine viral diarrhea virus 1-NADL, Bovine viral diarrhea virus1-Osloss, Bovine viral diarrhea virus 1-SD1, Bovine viral diarrhea virus2-C413, Bovine viral diarrhea virus 2-New York '93, Bovine viraldiarrhea virus 2-strain 890, Classical swine fever virus—Alfort/187,Classical swine fever virus—Alfort-Tübingen, Classical swine fevervirus—Brescia, Classical swine fever virus—C, Pestivirus of giraffe,Hepatitis C virus, including genotype 10, genotype 11, genotype 1a,genotype 1b, genotype 2a, genotype 2b, genotype 3a, genotype 4a,genotype 5a, genotype 6a, and GB virus B, GB virus A, GB virus C, andHepatitis G virus-1.

Flavivirid viruses particularly contemplated for use herein include,Dengue virus, Yellow fever virus, St. Louis encephalitis virus, Japaneseencephalitis virus, Murray Valley encephalitis virus, West Nile virus,Rocio virus, Tick-borne encephalitis virus, Omsk hemorrhagic fevervirus, Kyasunur Forest disease virus, Powassan virus, Pestiviruses, andHepatitis C virus.

Other RNA viruses contemplated herein which can be treated to produce avaccine as contemplated herein include, but are not limited to,Astroviruses, Norwalk-like viruses, Hepatitis D and E viruses, Nipahvirus, LR1 virus and Benyviruses.

The present invention also contemplates novel strains of WNV (OK03,OK02) for use in producing a vaccine.

The present invention also contemplates novel primers and their use inrecognizing and amplifying all of or portions of the WNV genome fordiagnosing WNV infections, for quality control of the vaccine, or foridentifying the presence of WNV in blood or blood products.

Currently there exists no FDA-approved vaccine against WNV for human useand there exist no FDA-approved vaccines against NIAID category A andcategory B priority viruses for human use. These agents have beenidentified by the US government (NIH) as most likely to be altered andabused as weapons for bioterrorism attacks. Hence, it is necessary to beable to detect these known agents and any novel derivatives, natural orengineered, and to speedily develop and deploy a vaccine against them.Chemical inactivation by MB is a more speedy means to develop a vaccineagainst abused, altered or emerging agents than genetically engineeredlife vaccines or recombinant protein-based formulations.

Strains OK02 and OK03 described herein are more recent isolates of WNVthan available from prior research and are representative of theclade/type of WNV that is responsible for the current epidemic in theUS. Strains OK02 and OK03 were deposited with the ATCC in the AmericanType Culture Collection (ATCC) located at 1081 University Boulevard,Monassas, Va., 20110-2209, USA, on Dec. 14, 2006, and have ATCCaccession numbers PTO-8079 and PTA-8078, respectively.

Prior to the present invention, it was not known whether or not WNV isaffected by treatment with MB with light. Herein it is shown thattreatment of WNV with MB and light inactivates the virus and that theinactivated WNV (or other Flavivirids or other RNA viruses) canstimulate an antibody response.

The vaccines produced according to the processes described herein offerthe following improvements over current vaccines: there is currently novaccine against WNV or other Flavivirid viruses that is approved forhuman use. Further, there is currently no vaccine against NIAID categoryA or B priority pathogenic viruses that is approved for human use. Sincethe pathogenicity of the virus in these vaccines is completelyinactivated, the vaccines of the present invention offer a superiorsafety profile over live-virus, attenuated vaccines. Thechemically-inactivated vaccines contemplated herein can never revert toor be reengineered to wild-type/virulent virus, nor can the vaccine,once distributed be re-isolated and amplified for malicious purposes orfor the purpose to infringe upon the original product.

Furthermore, chemically-inactivated vaccines are safe for use inimmunocompromised patients (e.g., children, transplant recipients, AIDSpatients, and individuals suffering from immunosuppressive conditionssuch as malaria, malnutrition and co-infection with other viruses orparasites). The preferred chemical described herein (MB), which is usedfor inactivation is without any side effects in humans and has been usedin patients since the 1750's to investigate kidney function. Chemicalinactivation allows (1) the production of seasonal vaccines with easeand no prior knowledge about the biology of the target, (2) theproduction of vaccines at low cost, and (3) the production of vaccinesat rapid speed, such as is needed in the event of a bioterrorist attack.The inactivation of the RNA genome yields a superior vaccine relative toinactivation of protein e.g., by formalin as introduced by J. Salk.Protein crosslinking changes the structure of the outer viralglycoproteins, which are the target for neutralizing antibodies. Hence,many epitopes presented by a chemically cross-linked vaccine differ fromepitopes presented by the live virus and hence lower vaccine efficacy.The mechanism described herein does not affect the outer glycoproteinsand hence yields a superior target that is more similar to wild-typevirus than a protein-crosslinked vaccine and is expectedly more potent.

While the RNA-crosslinking chemicals (e.g., MB, squalene) have beenproposed herein for the inactivation of WNV, other Flavivirids, or otherRNA viruses, herein they are not FDA approved or in active use forpatients. The RNA-crosslinking chemical (e.g., MB, squalene) have beenproposed for the inactivation of other viruses, but those disclosures donot cover further use of the inactivated viruses in a vaccine. StrainsOK02 and OK03 are more recent isolates of WNV and representative of theclade of WNV that is responsible for the current epidemic in the UScompared to, for example, strain NY99, which forms the basis of manyprior or ongoing vaccine efforts.

The WNV primer set of the present invention is the only WNV primer setthat can (1) amplify the complete WNV genome and yield pieces of a sizesuitable for rapid sequencing from mosquitoes, birds, other animals andhumans, that can (2) be used for quantitative real-time PCR basedquantification of virus for diagnosis, quality control of vaccines, as atool for high-throughput drug screens and to yield products for straintyping and sequencing, and (3) that can be used simultaneously for thetwo different purposes set forth herein. Currently, at least twodifferent primer sets are required to accomplish either.

Methods described below, though specific for WNV, can be applied to anyof the RNA viruses described elsewhere herein, particularly thosemethods related to virus inactivation and vaccine production.

Methods

Specimens: (a) RNA was obtained from 56 WNV-positive mosquito pools(both Aedes and Culex species) stored at −80° C. from the 2002 and 2003season. (b) Tissues (brain, kidney, heart) were obtained from 12individual WNV-infected blue jays available for re-isolation of otherWNV strains. (c) Two WNV strains (OK02, OK03) were isolated that grow inculture.

Clarified suspensions of tissue were prepared by placing the tissuesamples into 5 ml snap top tubes (FALCON 352063) together with 2 ml ofhomogenization buffer (2×PBS with 0.05M Tris/HCl pH 7.6, 1% (w/v) bovineserum albumin, 4.2 mM sodium bicarbonate, 0.1 μg/ml streptomycin, and 1μg/ml amphotericin B) and four copper clad steel beads (4.5 mm), thenvortexed for 5 times 45 s. The homogenate was subsequently centrifugedin 2 ml tubes (Sarstedt, Germany) at 13,000 rpmi in an eppendorfcentrifuge for 5 min to remove solids from the supernatant (SN).

WNV RNA isolation and cDNA synthesis: RNA was isolated as previouslydescribed (Fakhari, F. D., and D. P. Dittmer. 2002). cDNA wassynthesized as per our published procedures (Dittmer, D. P. 2003; Papinet al., 2004). Briefly, 500 ng of RNA was reverse transcribed in a 20 μlreaction with 100 U of SUPERSCRIPTII reverse transcriptase (INVITROGENINC., Carlsbad Calif.), 2 mM deoxyribonucleoside triphosphates, 2.5 mMMgC₁₂, 1 U of Rnasin (all from APPLIED BIOSYSTEMS, Foster City, Calif.),and 0.5 μg of appropriate primers (see below). The reaction mix wassequentially incubated at 42° C. for 45 min, 52° C. for 30 min, and 70°C. for 10 min. The reverse transcription reaction was stopped by heatingto 95° C. for 5 minutes. Net, 0.5 U RnaseH (INVITROGEN INC., Carlsbad,Calif.) was added, and the reaction incubated at 37° C. for anadditional 30 min. Afterwards, the cDNA pool was diluted 25-fold withdiethyl pyrocarbonate (DEPC)-treated, distilled H₂O and stored at 80° C.

Real-time QPCR for viral load: cDNA is analyzed for WNV following ourpreviously established procedures (Dittmer, D. P., 2003; Fakhari, F. D.,and D. P. Dittmer, 2002) with the exception that we use the ABIHighFidelity polymerase mix (APPLIED BIOSYSTEMS, INC.) rather than TaqPolymerase which has a lower fidelity and may lead to sequence errors(Malet, et al., 2003). The final PCR reaction contains 2.5 μl of forwardand reverse primer (final concentration 300 nM each), 7.5 μl of 2×PCRmix (2U HighFidelity polymerase, nucleotides and Mg according to themanufactures recommendations), and 5 μl of cDNA. Real-time PCR arepreformed using an ABI PRIZM5700 or ABI PRIZM7700 machine (APPLIEDBIOSYSTEMS, Foster City, Calif.) and universal cycling conditions (2 minat 50° C., 10 min at 95° C., 40 cycles of 15 sec at 95° C., and 1 min at60° C.). CT values are determined by automated threshold analysis.

Sequencing of PCR products: Real-time QPCR products were sequenced aftersubcloning into pCR2.1 (INVITROGEN INC.) according to the manufacturersprocedures, and transformed into DH5alpha cells. Positive clones wereidentified by IPTG/X-gal screening and miniprep DNA prepared using theBIORAD miniprep kit (BIORAD INC.). Inserts were identified by EcoRI andXbaI/HindIII digest and positive clones were subjected to sequencingusing M13forward and M13reverse primers, the primer binding sites forwhich are present in the pCR2.1 vector.

Sequence analysis: Sequences were determined by standard methods.

Mouse infection and pathology: Mice were housed in HEPA filtered BSL-3certified cages (BIOZONE INC.). Groups of mice were injected with WNVstrain OK02 or OK03. Mice were observed daily. Hind leg paralysis wasdetermined by observation, and such mice are unable to walk if nudgedgently. Paralyzed mice were euthanized by CO₂ generated from cylindersaccording to AAALAC regulations.

MB inactivation of West Nile Virus. 1 ml aliquots of WNV at aconcentration of 10⁷ pfu were mixed with MB (SIGMA INC.) to achieve thedesired final concentration of MB in the reaction mixture. Mixtures wereincubated for 20 minutes in the dark at room temperature and thensubsequently for 10 minutes at 10 cm distance from a 40 watt fluorescentwhite culture hood light at room temperature. Samples were then dilutedto the desired concentration of WNV for plaque assay. Inactivated viruswas prepared fresh for each assay and never kept for longer than 2 hoursat 4° C. before use. It is contemplated that other RNA viruses asdescribed herein can be similarly treated for vaccine formation.

Plaque Assays. Five-fold serial dilutions of WNV strains eithermock-treated or treated with MB were placed onto Vero cell monolayerscultured in either 6-well plates or T25 culture flasks (GREINER INC.).Virus aliquots were allowed to attach to the cells for 1 hour at normalcell culture conditions. After one hour the virus was aspirated from thecells. The monolayers were washed twice with phosphate-buffer saline(PBS) and overlayed with 2 ml or 5 ml (6-well or T25, respectively) of1% methylcellulose (SIGMA INC.) medium supplemented with 2% calf serum.Cells were incubated for 5 days. Afterwards the methylcellulose wasremoved, the monolayers were washed once with PBS and fixed with 100%ice-cold methanol for 5 minutes. The monolayers were subsequentlystained with 0.5% Giemsa stain (SIGMA INC.) and plaques counted using aMZ12 dissecting microscope (LEICA INC., Gemany).

Animal Studies. Normal BalbC/j mice ranging in age from 6-8 weeks wereobtained from JACKSON LABORATORIES (Bar Harbor, Me.). Severely combinedimmunodeficient (SCID) mice also 6-8 weeks in age were purchased fromTACONIC FARMS (Germantown, N.Y.). Mice were kept in groups of 5 animalsper cage. We used filter-top cages inside a laminar flow hood/rack and aBSL-3 certified mouse cage unit (BIOZONE INC.). All manipulations ofanimals and the changing of cages were performed inside a biosafetycabinet following BSL-3 procedures. The mouse facilities were fullyaccredited by the American Association for Accreditation of LaboratoryAnimal Care (AAALAC). Studies were approved by the local institutionalAnimal Care and Use Committee (IACUC). Mice were infected with 10⁴plaque-forming units (pfu) of mock-treated WNV or WNV treated with MB byi.p. injection in a total volume of 200 μl. Animals were monitored dailyand sacrificed when signs of hindleg paralysis or loss of mobilitybecame apparent.

Results

(A) Isolation of WNV Strains OK02 and OK03 by Plaque Assay on VeroCells.

We isolated and sequenced WNV from a 2002 Oklahoma isolate (OK02) andfrom a 2003 Oklahoma isolate (OK03) (see FIG. 1). The isolate wasobtained from an infected blue jay and passaged twice on Vero cells. RNAwas isolated, reverse-transcribed and PCT-amplified. The amplifiedproduct was sequenced directly using both primers. Direct comparison ofoverlapping sense and anti-sense sequences yielded 100% sequenceidentity for the PCR product (data not shown). A blastn comparison ofOK02 and OK03 identified a number of nucleotide changes relative tostrain NY-99 (including, but not limited to, those in Table 1). Thecomplete sequence of NY99 (Genbank Accession No. AF 196835.2) is herebyexpressly incorporated by reference herein in its entirety.

TABLE 1 Comparisons of OK02 and OK03 Genetic Sequences with Strain NY-99of WNV. Sequenced Size No changes Change orf aa change OK03 comparisonto WNV NY-99 strain (AF196835.2)  844-1230* 387 0 — — M & ENV — — 2628-3107* 505 1 2832 t < c NS1 — —  2158-2647* 490 2 2394 t < c ENVdel 717-728 2466 c < t ENV del 717-728  5571-6061* 492 1 5804 ins < aNS3 del 1903 1724-1914 191 3 1832 g < t ENV n/a 1868 c < t ENV n/a 1901t < c ENV n/a 2222-2168 55 0 — — ENV n/a 7809-8042 234 5 7820 g < delNS5 n/a 7938 t < c NS5 n/a 8001 t < c NS5 n/a 8034 t < c NS5 n/a 8026 g< t NS5 n/a 8312-8060 253 0 — — NS5 n/a 5803-5715 89 0 — — NS3 n/a5303-5431 129 0 — — NS3 n/a OK02 comparison to WNV NY-99 strain(AF196835.2)  844-1229* 386 0 — — M & ENV — —  1724-2222* 499 1 2121 g <a ENV — —  7809-8312* 504 3 7938 t < c NS5 — — 8189 a < g NS5 2698 D < G8193 g < a NS5 2699 INS < W  9604-10110* 507 0 — — NS5 — — 5803-5467 3361 5455 t < c NS3 n/a 5303-5497 195 1 5416 a < g NS3 n/a 2628-2943 316 12924 g < t NS1 n/a 3131-2945 187 0 — — NS1 n/a 4605-4859 255 2 4803 c <t NS3 n/a 4845 t < c NS3 n/a 5112-4923 191 2 4960 t < c NS3 n/a 4962 ins< c NS3 n/a 2152-2287 136 0 — — ENV n/a 2647-2407 241 2 2466 g < a ENVn/a 2446 g < a ENV n/a *assembled pair (forward and reverse sequencing)

(B) Inactivation of WNV Strain OK02 and OK03 by Methylene Blue+Light.

As a member of the Flaviviridae family of viruses, WNV utilizes a RNAdependent RNA polymerase for replication. This process is relativelyerror prone and can lead to the creation of multiple strains. To testthe ability of MB to inactivate multiple WNV strains, MB was testedagainst multiple strains of WNV, including OK02, OK03 and NY-99 (the1999 prototype virus NY-99 and the more recent Oklahoma isolates from2002 and 2003). 5×10³ pfu of OK03 WNV was incubated with 2 μM MB andlight. The comparison of the inactivation of OK03 and OK02 is shown inFIG. 2. As observed, MB above 2 μM reduced the viral activity of theOK02 strain of WNV by ≧10³ (FIG. 2, panel A). This held true for theOK03 strain of WNV virus (FIG. 2, panel B) as well as for the NY-99strain (data not shown). This demonstrates the efficacy of MB tophoto-inactivate different strains of WNV. It is contemplated that otherRNA viruses as described herein can be similarly treated for vaccineformation.

(C) Safety of the WNV Vaccine in Mice

OK02 WNV was tested for its ability to cause mortality and morbidity inmice. It was previously published that ≦10⁴ pfu of WNV i.p. are lethalin BalbC/j mice with an average survival time of 9 days (Kramer, L., andK. Bernard. 2001). Using this study as a guideline we infected one groupof BalbC/j mice (n=5) with a dose of 10⁴ pfu/animal of WNV strain OK02.By day nine only 40% of the mice were alive. By day 10 all mice (100%)had succumbed to infection, yielding a mean survival of time of 9.4 daysconsistent with previously published studies (FIG. 3, panel A, blackdots). We then tested the ability of MB to block WNV strain OK02 lethalinfection in mice. Reinforcing the results obtained tissue culture basedassays for WNV infectivity, 100% of the mice infected with 10⁴ pfu of 20μM MB-treated WNV were still alive at day 15 (FIG. 3, panel A, graysquares). It is contemplated that vaccines for other RNA viruses asdescribed herein can be similarly used for inoculation. The differencein survival was significant to p≦0.0015 at day 15 using Student'st-test.

An active immune system within the BalbC/j mice could contribute toblocking infection in the MB treated group. It is possible that if onlya few infectious particles survived the MB photo-inactivation then hostimmune response would impede the disease. To rule out this possibility,we repeated the experiment using severe-combined immune deficient (SCID)mice. Two groups of C.B. 17-SCID mice (n=5 per group) were infected i.p.with 10⁴ pfu of MB-treated or mock-treated virus. 60% of themock-treated group succumbed to infection by day 8, and all mice in thisgroup were dead by <9 days (FIG. 3, panel B, black dots). This yields amean survival of less than 9 days, which was almost identical to that ofthe BalbC/j mice. Similar to the BalbC/j mice animals injected withMB-treated WNV survived to day 15 and beyond days (FIG. 3, panel B, graysquares). At day 15 p.i. we calculated p≦0.0023 by Student's t-test.This result rules out the possibility that host immunity played a rolein stopping WNV disease in these mice and established the 20 μM MB canstop WNV-associated morbidity and mortality in vivo.

(d) Efficacy of WNV Vaccine in Mice

As shown in FIG. 4, we have established a mouse model for WNV usingimmune competent BALB/cJ and immunodificient C.B.17-SCID mice. Usingi.p. injection of 10⁴ pfu WNV strain OK02, we found that 100% of BALB/cJand 100% of C.B.17 SCID mice succumb to infection as measured byKaplan-Meier plot (FIG. 4, panel A and B). The mice develop hind-legparalysis and present with encephalitis at autopsy (data not shown).Regardless of the host immune status (naïve, SCID, immunized/2infection) mice that succumb to WNV infection die between eight and ninedays suggesting that in those animals the virus overwhelms the hostresponse.

A single exposure of 10⁴ pfu of MB-inactivated WNV vaccine significantlyprotects against diseases and delays mortality upon subsequent challengewith 10⁴ pfu live virus (FIG. 4, panel C). As expected, exposure ofimmunodeficient SCID mice to chemically inactivated WNV (FIG. 4, panelD) did not protect from subsequent infection. This shows thatMB-inactivated WNV vaccine acts by using the host adaptive (B cells andT cells) host immune system, which is not present in SCID mice.

In people, WNV infection causes high titer antibodies of type IgM andIgG. These neutralize and ultimately clear the virus leading toresolution of infection and disease. The present West-Nile virus vaccineinduces high titer IgM and IgG antibodies (FIGS. 6 and 7, respectively).The induction of such antibodies by a vaccine is a major indicator ofvaccine efficacy. Anti-WNV antibodies are considered for therapeutic useand proven to prevent WNV infection in mice (Gould, 2005; Oliphant,2005). We pooled the sera from mice that were immunized with MB+WNV,challenged with WNV and survived (FIG. 8) and tested for the presence ofanti WNV antibodies of type IgG and type IgM using the FDA-approvedELISA (FOCUS INC.). Pooled mouse sera were diluted in saline asindicated and tested (in duplicate) for reactivity according to themanufacturers recommendations. Also included were positive and negativecontrols. An index value of 1.0 for IgM and for IgG was consideredpositive. This establishes end-point dilution titers of 1:12,500, whichis comparable to titers obtained by other vaccine candidates (Ledizet,2005). West-Nile virus vaccine protects mice against infection afterinter muscular (i.m.) and inter peritoneal (i.p.) inoculation. Werepeated our mouse vaccination experiment with a second set of miceusing either intra muscular or intra peritoneal immunization of 10³ pfuWNV & MB. As shown in FIG. 8, both routes of immunization protected micefrom subsequent challenge (p≦0.05 by t-test).

(e) Real-Time Quantitative RT-PCR Across the WNV Genome

To expand upon this development we designed real-time quantitativeRT-PCR primers that, in combination, span almost the entire WNV genome(FIG. 5). In contrast to prior published work, all of the primer pairsused herein (see Table 2, SEQ ID Nos. 1-18) work the same, at highlystringent annealing temperature of 60° C. and therefore can be utilizedin a 96 well high-throughput format. We have adapted PCR conditions suchthat these primers will yield a product even when up to three nucleotidemismatches are present in the primer binding site.

TABLE 2 Oligonucleotide Primers Used in RT-PCR Genome SEQ Product StartID Direction Size (bp) Position* Length Tm GC % Sequence 1 Forward 4991724 20 59.02 50.00 TAGCATTGGGCTCACAAGAG 2 Reverse 499 2203 20 58.9955.00 GCTAGTCTCTGCGCTCCTTT 3 Forward 504 7809 20 58.85 45.00CAGGAAAGAAGGCAATGTCA 4 Reverse 504 8293 20 59.00 55.00AGTGGGTTTCTGACCAGTCC 5 Forward 501 5303 20 58.70 50.00AGATGGCTGAAGCACTGAGA 6 Reverse 501 5784 20 59.05 50.00ATTTTGGGTACTCCGTCTCG 7 Forward 504 2628 20 58.91 55.00AGTGTGCGGTCTACGATCAG 8 Reverse 504 3112 20 58.85 50.00TTGACTTCACCCAGAACTGC 9 Forward 508 4605 20 58.94 50.00AAAGAGAGGAGGCGTGTTGT 10 Reverse 508 5093 20 59.12 50.00CTGCACTATCGCGCTTATGT 11 Forward 496 2152 20 59.29 50.00CATTGGCACAAGTCTGGAAG 12 Reverse 496 2628 20 58.91 55.00CTGATCGTAGACCGCACACT 13 Forward 491 5571 20 59.09 50.00AGGCACTTCAGATCCATTCC 14 Reverse 491 6042 20 58.88 50.00AGTCGTCTTCATTCGTGTGC 15 Forward 507 9604 20 58.94 45.00AAAGGGAAAGGACCCAAAGT 16 Reverse 507 10091 20 58.75 55.00TGTCATCCACTCTCCTCCTG 17 Forward 200 844 20 56.00 55.00TGGATCTTGAGGAACCCTGG 18 Reverse 200 1209 21 GGGTCAGCACGTTTGTCATTG *=Genome position according to WNV NY99 complete genome sequence(Lanciotti, et al., 1999).

These experiments demonstrate the efficacy of MB to photoinactivate WNVin tissue culture and, for the first time, demonstrate the absence ofresidual infectivity in an animal model of WNV infection. This result isconsistent with prior work on MB (Mohr et al., 2004) and extends thosestudies in important ways including: (i) MB+light was able to inactivatemultiple independent low-passage isolates of WNV from recent outbreaks2002 and 2003; (ii) we determined the IC₅₀ to be 0.10 μM; when aconcentration of 20 μM MB was used a reduction of 10⁷ pfu was achieved,which is higher than any WNV titer found in human blood products todate; (iii) MB+light-inactivated virus was no longer infectious in ananimal model of WNV infection.

Laboratory mice are very sensitive to WNV infection (Beasley et al.,2002; Kramer and Bernard, 2001; Perelygin et al., 2002; Samuel, 2002).As little as 1 pfu/animal can be lethal and 10³ pfu causes mortality in100% of infected animals within 7-8 days. MB+light treatment completelyblock-associated morbidity and mortality at challenge doses of 10³ and10⁴ pfu per animal. MB has been used in the treatment of humans for manyyears. It is safe with the longest reported oral use for up to 19 monthsat 100 mg/kg (˜50 μM in blood) twice daily with no reported side effects(Naylor et al., 1986). DiSanto and Wagner (1972) report that MB isabsorbed orally and has a half-life of about 10 h. The in vivo half-lifefor MB +light-inactivated WNV still remains to be established, but ouranimal experiments imply that MB+light-inactivated WNV particles have notoxic side effects either. Use of this technology to inactivate a widerange of viruses in blood products will help to lessen theever-increasing threat of viral infection from blood transfusion. Itshould also be noted that while blood is currently tested for infectiousagents such as HIV-1, hepatitis C, and WNV; the blood units which testpositive cannot be used. MB+light inactivtion technology could combatblood shortages by rendering these once useless blood samples usefulagain. This is particularly useful in developing nations or in a time ofwar.

Utility

The present invention in one embodiment is directed to vaccines againstRNA viruses, in particular RNA viruses in the family Flaviviridae, whichincludes for example West Nile Virus, Yellow fever virus, Dengue fevervirus, Hepatitis C virus, Pestiviruses, Bovine viral diarrhea virus, andClassical Swine fever virus (and others as described herein), thevaccine comprising an RNA virus or immunogenic portions thereof, whichhave been treated and rendered inactive by Methylene Blue (MB), orderivatives thereof, and visible light. Similarly the RNA virus orimmunogenic portion thereof may have been inactivated by otherphenothiazine dyes, including Methylene Green, 1-methyl MB, 1,9-dimethylMB, Azure A, Azure B, Azure C, thionine, and toluidine blue, or bysqualene. More broadly, the invention comprises a vaccine or compositioncomprising one or more RNA viruses which have been inactivated bychemicals which induce RNA:RNA or RNA:protein crosslinking.

Further, the invention contemplates vaccines produced via the aboveinactivation techniques which are directed against any RNA virusincluding, but not limited to influenza, HIV and NIAID category A andcategory B priority pathogenic viruses or any other RNA virus describedherein.

The present invention also contemplates novel strains of WNV (OK02 andOK03) which can be used herein in to produce a vaccine.

The present invention also contemplates and describes herein novelprimers and their use in recognizing and amplifying all of or portionsof the WNV genome for diagnosing WNV infections or for identifying thepresence of WNV in blood or blood products, or that can recognize andamplify the entire viral genome of the NIAID category A or B prioritypathogens.

More particularly, the present invention provides a vaccine compositionwhich comprises an effective immunizing amount of an immunogenicallyactive component selected from the group consisting of one or moreinactivated whole, subunits or portions, of a West Nile Virus(including, but not limited to, WNV strains NY-99, OK02 and OK03 orothers indicated below), an antigen derived from said virus, and amixture thereof; and a pharmacologically acceptable carrier wherein thewhole virus, portion, or subunit or antigenic component thereof wasprovided by inactivating the one or more strains of West Nile Virus orcomponents thereof by exposure to Methylene Blue (or other dyes orcompounds described herein) and visible light. WNV strains that could betreated as described herein to produce an inactive immunogenic WNVvaccine include but are not limited to OK02, OK03, NY99, Cm-CT99,Crow-NJ99, Crow-NY99, C.pipiens-NY99, Eq.-NY99, HB709-NY99, HB743-NY99,US AMRIID99, and 2741.

The present invention also provides a method for the prevention oramelioration of a disease caused by a particular RNA virus in a human oranimal subject which comprises administering to said subject an RNAvirus vaccine composition as described above disposed in apharmacologically acceptable carrier to induce an immunogenic responseeffective against the RNA virus in vivo.

As used herein, the term “immunogenic or immunogenically active”designates the ability to stimulate an immune response, i.e., tostimulate the production of antibodies, particularly humoral antibodies,or to stimulate a cell-mediated response. For example, the ability tostimulate the production of circulating or secretory antibodies or theproduction of a cell-mediated response in local mucosal regions, (e.g.,intestinal mucosa), peripheral blood, cerebral spinal fluid or the like.

The effective immunizing amount of the immunogenic or immunogenicallyactive component may vary and may be any amount sufficient to evoke animmune response and provide immunological protection against an RNAvirus disease as contemplated herein. Amounts wherein a dosage unitpreferably comprises at least about 1×10³ to 1×10⁴ TCID₅₀ (TissueCulture Infective Dose) of inactivated (i.e., treated as describedherein) whole or subunit virus cells or antigen derived therefrom or amixture thereof, and preferably at least about 1×10⁵ TCID₅₀, aresuitable. Even more preferably, at least about 1×10⁶ TCID₅₀, aresuitable. Even more preferably, at least about 1×10⁷ TCID₅₀ per dosageunit may be utilized. It is especially desirable that at least about1×10⁸ TCID₅₀ of inactivated whole or subunit RNA virus cells or antigenderived therefrom or a mixture thereof be used in the vaccinecomposition of the invention. In certain embodiments, as much as 1×10⁹TCID₅₀ or 1×10¹⁰ TCID₅₀ and more may be utilized. A quantity in therange of about 1×10⁴ TCID₅₀ to about 1×10⁸ TCID₅₀ is preferablyutilized.

At least one dosage unit per subject is contemplated herein as avaccination regimen. In some embodiments, two or more dosage units maybe especially useful. A dosage unit of vaccine composition may typicallybe about 0.1 to 10 milliliters, preferably about 0.5 to 5 milliliters,and even more preferably about 1 to 2 milliliters, with each dosage unitcontaining the heretofore described quantity of virus or viruscomponent. The skilled artisan will quickly recognize that a particularquantity of vaccine composition per dosage unit, as well as the totalnumber of dosage units per vaccination regimen, may be optimized, solong as an effective immunizing amount of the virus or a componentthereof is ultimately delivered to the subject.

The RNA virus vaccine composition of the present invention may alsocontain one or more adjuvants or excipients. As used herein the term“adjuvant” refers to any component, which improves the body's responseto a vaccine. The adjuvant will typically comprise about 0.1 to 50%vol/vol of the vaccine formulation of the invention, more preferablyabout 1 to 50% of the vaccine, and even more desirably about 1 to 20%thereof. Amounts of about 4 to 10% may be even more preferred. Adjuvantsare well known in the art thus further detailed description thereofherein is not deemed necessary.

In addition, the adjuvant may include one or more wetting or dispersingagents in amounts of about 0.1 to 25%, more preferably about 1 to 10%,and even more preferably about 1 to 3% by volume of the adjuvant.Particularly preferred as wetting or dispersing agents are non-ionicsurfactants. Useful non-ionic surfactants includepolyoxyethylene/polyoxypropylene block copolymers, especially thosemarketed under the trademark PLURONIC® and available from BASFCorporation (Mt. Olive, N.J.). Other useful nonionic surfactants includepolyoxyethylene esters such as polyoxyethylene sorbitan monooleate,available under the trademark TWEEN 80®. It may be desirable to includemore than one, e.g., at least two, wetting or dispersing agents in theadjuvant as part of the vaccine composition of the invention.

Other components of the adjuvant may include such preservative compoundsas formalin and thimerosal in amounts of up to about 1% vol/vol of theadjuvant.

Pharmacologically acceptable carriers suitable for use in the vaccinecomposition of the invention may be any conventional liquid carriersuitable for pharmaceutical compositions, preferably a balanced saltsolution, physiological saline, or other water-based solution suitablefor use in tissue culture media. Other available carriers well known tothose of ordinary skill in the art may also be utilized.

Additional excipients available and known to those of ordinary skill inthe art may also be included in the vaccine composition according to thevarious embodiments heretofore described. For example, pH modifiers maybe utilized.

The components of the vaccine composition of the invention as heretoforedescribed, including the carrier, may be combined together usingtechniques known to those of ordinary skill in the art.

In one embodiment of the invention the immunogenically active componentof the invention may be incorporated into liposomes using knowntechnology such as that described in Nature, 1974, 252, 252-254 or theJournal of Immunology, 1978, 120, 1109-13. In another embodiment of theinvention, the immunogenically active component of the invention may beconjugated to suitable biological compounds such as polysaccharides,peptides, proteins, polymers or the like, or a combination thereof.

In a preferred embodiment of the invention, the novel vaccinecomposition contemplated herein may be formulated in a dosage unit formas heretofore described to facilitate administration and ensureuniformity of dosage. Formulation may be effected using availabletechniques, such as those applicable to preparations of emulsions.

The novel vaccine composition contemplated herein may be administered,for example, by one or more of parenterally, intramuscularly,subcutaneously, intraperitoneally, intradermally, orally, intranasally,arterially, intraocularly, rectally, intralymphnodally, or vaginally,preferably in effective amounts according to a schedule which may bedetermined by the time of anticipated potential exposure to a carrier ofor infection by any of the RNA viruses described herein. In this way,the subject may have time to build immunity prior to the naturalexposure. By way of non-limiting example, a typical treatment scheduleor dosing regimen may include parenteral administration, preferablyintramuscular injection of one dosage unit, at least about 2-8 weeksprior to potential exposure. At least two administrations may bepreferred, for example one dosage unit at about 8 weeks and a seconddosage unit at about 3-5 weeks prior to potential exposure of thetreated subject. As heretofore set forth, a dosage unit will typicallybe within the range of about 0.1 to 10 milliliters of vaccinecomposition containing the previously described amounts of active andpercentages of adjuvant and inactives set forth. A dosage unit withinthe range of about 0.5 to 5 milliliters is perhaps more preferred, withabout 1 to 2 milliliter(s) being particularly preferred.

The subjects which may be treated with the RNA virus vaccinecontemplated herein include, but are not limited to, mammals, includingprimates such as humans, chimpanzees, baboons, gorillas and orangutans,monkeys and lemurs; mustelids including minks; camelids, includingcamels, llamas, alpacas, and vicunas; felids including lions, tigers anddomestic cats; canids including dogs; bovids including cattle; equidsincluding horses; ovids including sheep and goats; suids including pigs;cervids including deer, elk and moose; and birds including chickens,turkey, ostriches, ducks, geese, pigeons, and parrots.

The present invention is not to be limited in scope by the specificembodiments described herein, since such embodiments are intended as butsingle illustrations of one aspect of the invention and any functionallyequivalent embodiments are within the scope of this invention. Indeed,various modifications of the methods of the invention in addition tothose shown and described herein will become apparent to those skilledin the art form the foregoing description.

Cited References:

Each of the references, patents or publications cited herein isincorporated by reference in its entirety.

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CDC, 2002. West Nile Virus Activity-United States, Jul. 31-Aug. 7, 2002,and Louisianna, Jan. 1-Aug. 7, 2002. MMWR Morbid, Mortal. Wkly. Rep. 51,681-683.

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Lanciotti, R. S., Roehrig, J. T., Deubel, V., Smith, J., Parker, M.,Steele, K., et al., 1999. Origin of the West Nile virus responsible foran outbreak of encephalitis in the northeastern United States. Science286, 2333-2337.

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1. A method for inducing an immune response against an RNA virus in asubject, comprising: administering to the subject an immunogeniccomposition comprising: an RNA virus or an immunogenic portion thereofwherein the RNA virus or immunogenic portion thereof has beeninactivated by exposure to a phenothiazine dye and visible light; and apharmaceutically acceptable carrier or excipient.
 2. The method of claim1 wherein the phenothiazine dye used to inactivate the RNA virus orimmunogenic portion thereof is Methylene Blue, Methylene Green, 1-methylMethylene Blue, 1, 9-dimethyl Methylene Blue, Azure A, Azure B, Azure C,thionine, toluidine blue, or squalene.
 3. The method of claim 1 whereinthe composition further comprises an adjuvant.
 4. The method of claim 1wherein the composition comprises at least one additional strain of theRNA virus or immunogenic portion thereof, or at least one additionalspecies of RNA virus or an immunogenic portion thereof.
 5. The method ofclaim 1 wherein the subject is selected from the group comprisingmammals, including primates such as humans, chimpanzees, baboons,gorillas and orangutans, monkeys and lemurs, mustelids including minks,camelids including camels, llamas, alpacas, and vicunas, felidsincluding lions, tigers and domestic cast, canids including dogs, bovidsincluding cattle, equids including horses, mules and donkeys, ovidsincluding sheep and goats, suids including pigs, cervids including deer,elk and moose, and birds including chickens, turkey, ostriches, ducks,geese, pigeons, and parrots.
 6. The method of claim 1 wherein theimmunogenic composition is administered parenterally, intramuscularly,intraocularly, subcutaneously, intraperitoneally, arterially,intradermally, orally, intranasally, intralymphnodally, rectally,vaginally, or by a combination of these routes.
 7. A method for inducingan immunogenic response in a subject to a virus of the Flaviviridae,comprising: administering to the subject an immunogenic compositioncomprising: a Flavivirid virus or an immunogenic portion thereof whereinthe Flavivirid virus or immunogenic portion thereof has been inactivatedby exposure to a phenothiazine dye and visible light; and apharmaceutically acceptable carrier or excipient.
 8. The method of claim7 wherein the phenothiazine dye used to inactivate the Flavivirid virusor immunogenic portion thereof is Methylene Blue, Methylene Green,1-methyl Methylene Blue, 1, 9-dimethyl Methylene Blue, Azure A, Azure B,Azure C, thionine, toluidine blue, or squalene.
 9. The method of claim 7wherein the composition further comprises an adjuvant.
 10. The method ofclaim 7 wherein the composition comprises at least one additional strainof the Flavivirid virus or immunogenic portion thereof, or at least oneadditional species of Flavivirid virus or an immunogenic portionthereof.
 11. The method of claim 7 wherein the subject is selected fromthe group consisting of mammals, including primates such as humans,chimpanzees, baboons, gorillas and orangutans, monkeys and lemurs,mustelids including minks, camelids including camels, llamas, alpacas,and vicunas, felids including lions, tigers and domestic cast, canidsincluding dogs, bovids including cattle, equids including horses, ovidsincluding sheep and goats, suids including pigs, cervids including deer,elk and moose, and birds including chickens, turkey, ducks, geese,pigeons, and parrots.
 12. The method of claim 7 wherein the immunogeniccomposition is administered parenterally, intramuscularly,intraocularly, subcutaneously, intraperitoneally, arterially,intradermally, orally, intranasally, intralymphnodally, rectally,vaginally, or by a combination of these routes.